VMD

From MetaCentrum
Jump to navigation Jump to search

Description

VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation.


Notice: We recommend to use OnDemand to run this graphical application as interactive job.

License

free for academic use -- please read license at official site

Usage

module avail vmd/ # list available modules
module load vmd   # load (default) module

Notice: This application use or needs GUI – graphical interface. To use the application in graphical mode see Remote desktop or X-Window.

Documentation

http://www.ks.uiuc.edu/Research/vmd/current/docs.html

Homepage

http://www.ks.uiuc.edu/Research/vmd/